MLP 1.19.0
Tobias Verbeke
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MLP | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLP_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MLP.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘AnnotationDbi’ ‘affy’ ‘plotrix’ ‘gplots’ ‘gmodels’ ‘gdata’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MLP’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘Rgraphviz’ ‘annotate’ ‘org.Cf.eg.db’
‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘reactome.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘affy’ ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’ ‘plotrix’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGeneSetDescription: no visible binding for global variable ‘GOTERM’
addGeneSetDescription: no visible binding for global variable
‘KEGGPATHID2NAME’
addGeneSetDescription: no visible binding for global variable
‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
‘org.Mm.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Hs.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Rn.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Cf.egGO2ALLEGS’
getGeneSets: no visible binding for global variable ‘GOBPANCESTOR’
getGeneSets: no visible binding for global variable ‘GOMFANCESTOR’
getGeneSets: no visible binding for global variable ‘GOCCANCESTOR’
getGeneSets: no visible binding for global variable ‘GOTERM’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
getGeneSets: no visible binding for global variable
‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
‘reactomePATHID2EXTID’
plotGOgraph: no visible global function definition for ‘GOGraph’
plotGOgraph: no visible global function definition for ‘removeNode’
plotGOgraph: no visible global function definition for ‘nodes’
plotGOgraph: no visible global function definition for ‘layoutGraph’
plotGOgraph: no visible global function definition for ‘colorpanel’
plotGOgraph: no visible global function definition for
‘nodeRenderInfo<-’
plotGOgraph: no visible global function definition for ‘getGOTerm’
plotGOgraph: no visible global function definition for ‘edgeRenderInfo’
plotGOgraph: no visible global function definition for
‘edgeRenderInfo<-’
plotGOgraph: no visible global function definition for
‘graphRenderInfo’
plotGOgraph: no visible global function definition for
‘graphRenderInfo<-’
plotGOgraph: no visible global function definition for ‘renderGraph’
plotGOgraph: no visible global function definition for ‘smartlegend’
plotGeneSetSignificance: no visible global function definition for
‘lookUp’
Undefined global functions or variables:
GOBPANCESTOR GOCCANCESTOR GOGraph GOMFANCESTOR GOTERM
KEGGPATHID2EXTID KEGGPATHID2NAME colorpanel edgeRenderInfo
edgeRenderInfo<- getGOTerm graphRenderInfo graphRenderInfo<-
layoutGraph lookUp nodeRenderInfo<- nodes org.Cf.egGO2ALLEGS
org.Hs.egGO2ALLEGS org.Mm.egGO2ALLEGS org.Rn.egGO2ALLEGS
reactomePATHID2EXTID reactomePATHNAME2ID removeNode renderGraph
smartlegend
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [58s/59s] WARNING
Found the following significant warnings:
Warning: 'smartlegend' is deprecated.
Warning: 'smartlegend' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
MLP 28.266 0.239 28.534
getGeneSets 20.557 0.296 20.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.MLP.R’ [47s/47s]
[47s/47s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/MLP.Rcheck/00check.log’
for details.